You are correct in that Harvard graduates have better outcomes. However, we are talking about, as you said, students with 3.9 GPAs whose acceptance rates are close to 100% instead of 85%-90%.
I do think that a large part of that is both preference of Ivies for Ivy graduates, as well as better advising and more strategic applications. I think that Harvard pre-meds are much more likely to have “safety” options than UCB graduates, and to have more guidance during their undergrad.
All that being said, yes, you are correct in saying that not only MCAT and GPA matter, but also the undergraduate college.